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New Phytol. 2015 Oct;208(2):596-607. doi: 10.1111/nph.13471. Epub 2015 Jun 8.

Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size.

Author information

1
School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
2
Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK.
3
Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA.
4
Biology Centre CAS, Institute of Plant Molecular Biology, CZ-37005, České Budějovice, Czech Republic.
5
Plant Cytogenomics Research Group, CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic.
6
School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK.
7
Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK.

Abstract

Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.

KEYWORDS:

DNA deletion; Fritillaria; Liliaceae; genome size evolution; genome turnover; repetitive DNA; transposable elements (TEs)

PMID:
26061193
PMCID:
PMC4744688
DOI:
10.1111/nph.13471
[Indexed for MEDLINE]
Free PMC Article

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